Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Sven Heinz,Christopher Benner,Nathanael J. Spann,Eric Bertolino,Yin C. Lin,Peter Laslo,Jason X. Cheng,Cornelis Murre,Harinder Singh,Harinder Singh,Christopher K. Glass +10 more
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TLDR
It is demonstrated in macrophages and B cells that collaborative interactions of the common factor PU.1 with small sets of macrophage- or B cell lineage-determining transcription factors establish cell-specific binding sites that are associated with the majority of promoter-distal H3K4me1-marked genomic regions.About:
This article is published in Molecular Cell.The article was published on 2010-05-28 and is currently open access. It has received 9620 citations till now. The article focuses on the topics: Pioneer factor & General transcription factor.read more
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Transcriptional and epigenetic regulation of macrophages in atherosclerosis.
Tatyana Kuznetsova,Koen H.M. Prange,Christopher K. Glass,Menno P.J. de Winther,Menno P.J. de Winther +4 more
TL;DR: The emerging role of transcription factors and epigenetic remodelling in macrophages in the context of atherosclerosis and inflammation, and a comprehensive overview of epigenetic enzymes and transcription factors that are involved in Macrophage activation are discussed.
Journal ArticleDOI
Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA
Nicolas Léveillé,Carlos A. Melo,Carlos A. Melo,Koos Rooijers,Angel Diaz-Lagares,Sonia Melo,Gozde Korkmaz,Rui Lopes,Farhad Akbari Moqadam,Ana Maia,Patrick J. Wijchers,Geert Geeven,Monique L. den Boer,Raghu Kalluri,Wouter de Laat,Manel Esteller,Manel Esteller,Reuven Agami,Reuven Agami +18 more
TL;DR: Among p53-induced lncRNAs, LED is identified and it is demonstrated that its suppression attenuates p53 function, and its dysregulation in cancer is suggested.
Journal ArticleDOI
Dnmt3a and Dnmt3b Associate with Enhancers to Regulate Human Epidermal Stem Cell Homeostasis
Lorenzo Rinaldi,Debayan Datta,Judit Serrat,Lluis Morey,Guiomar Solanas,Alexandra Avgustinova,Enrique Blanco,José Ignacio Pons,David Matallanas,Alex von Kriegsheim,Luciano Di Croce,Salvador Aznar Benitah +11 more
TL;DR: It is shown that in human epidermal stem cells, the two proteins bind in a histone H3K36me3-dependent manner to the most active enhancers and are required to produce their associated enhancer RNAs.
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Base-resolution models of transcription factor binding reveal soft motif syntax
Žiga Avsec,Melanie Weilert,Avanti Shrikumar,Sabrina Krueger,Amr Alexandari,Khyati Dalal,Khyati Dalal,Robin Fropf,Charles McAnany,Julien Gagneur,Anshul Kundaje,Julia Zeitlinger,Julia Zeitlinger +12 more
TL;DR: A deep learning model is introduced that uses DNA sequence to predict base-resolution ChIP-nexus binding profiles of pluripotency TFs, and interpretation tools are developed to learn predictive motif representations and identify soft syntax rules for cooperative TF binding interactions.
Journal ArticleDOI
Epigenetic regulation of macrophages: from homeostasis maintenance to host defense.
TL;DR: This review focuses on key epigenetic events associated with macrophage fate, highlighting events related to the maintenance of tissue homeostasis, responses to different stimuli and the formation of innate immune memory.
References
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Artem Barski,Suresh Cuddapah,Kairong Cui,Tae-Young Roh,Dustin E. Schones,Zhibin Wang,Gang Wei,Iouri Chepelev,Keji Zhao +8 more
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RAG-1-deficient mice have no mature B and T lymphocytes
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TL;DR: The introduction of a mutation in RAG-1 into the germline of mice via gene targeting in embryonic stem cells is described and it is shown that this mutation either activates or catalyzes the V(D)J recombination reaction of immunoglobulin and T cell receptor genes.
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TL;DR: This study uses chromatin immunoprecipitation coupled with ultra-high-throughput DNA sequencing to map the locations of TF-binding sites and identifies important features of the transcriptional regulatory networks that define ES-cell identity.
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Genome-scale DNA methylation maps of pluripotent and differentiated cells
Alexander Meissner,Tarjei S. Mikkelsen,Tarjei S. Mikkelsen,Hongcang Gu,Marius Wernig,Jacob H. Hanna,Andrey Sivachenko,Xiaolan Zhang,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,David B. Jaffe,Andreas Gnirke,Rudolf Jaenisch,Eric S. Lander +14 more
TL;DR: Low-throughput reduced representation bisulphite sequencing is established as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.